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Journal of Virology, November 2002, p. 11273-11282, Vol. 76, No. 22
0022-538X/02/$04.00+0     DOI: 10.1128/JVI.76.22.11273-11282.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Human Immunodeficiency Virus Type 1 Recombination: Rate, Fidelity, and Putative Hot Spots

Jianling Zhuang,1 Amanda E. Jetzt,1,2,{dagger} Guoli Sun,1 Hong Yu,1,{ddagger} George Klarmann,3 Yacov Ron,1 Bradley D. Preston,4 and Joseph P. Dougherty1*

Department of Molecular Genetics and Microbiology, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854,1 Graduate Program in Microbiology and Molecular Genetics, Rutgers University, New Brunswick, New Jersey 08903,2 Department of Biochemistry and Radiation Oncology, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112,3 Department of Pathology, University of Washington, Seattle, Washington 981954

Received 2 May 2002/ Accepted 7 August 2002

Previously, we reported that human immunodeficiency virus type 1 (HIV-1) recombines approximately two to three times per genome per replication cycle, an extremely high rate of recombination given the relatively small genome size of HIV-1. However, a recombination hot spot involving sequence of nonretroviral origin was identified in the vector system utilized, raising the possibility that this hot spot skewed the rate of recombination, and the rate of recombination observed was an overestimation. To address this issue, an HIV-1-derived vector system was used to examine the rate of recombination between autologous HIV-1 sequences after restricting replication to a single cycle in the absence of this hot spot. Viral DNA and RNA were analyzed by a combination of the heteroduplex tracking assay, restriction enzyme analysis, DNA sequencing, and reverse transcription-PCR. The results indicate that HIV-1 undergoes recombination at a minimum rate of 2.8 crossovers per genome per cycle. Again, this is a very high rate given the small size of the HIV-1 genome. The results also suggested that there might be local hot spots of recombination at different locations throughout the genome since 13 of the 33 strand transfers identified by DNA sequencing shared the same site of recombination with one or two other clones. Furthermore, identification of crossover segments also allowed examination of mutations at the point of recombination, since it has been predicted from some studies of cell-free systems that mutations may occur with a frequency of 30 to 50% at crossover junctions. However, DNA sequence analysis of crossover junctions indicated that homologous recombination during viral replication was not particularly mutagenic, indicating that there are other factors or conditions not yet reproduced in cell-free systems which contribute to fidelity during retroviral recombination.

* Corresponding author. Mailing address: Department of Molecular Genetics and Microbiology, UMDNJ-Robert Wood Johnson Medical School, 675 Hoes Ln., Piscataway, NJ 08854. Phone: (732) 235-4588. Fax: (732) 235-5223. E-mail: doughejp{at}umdnj.edu.

{dagger} Present address: Tumor Biology Department, Schering-Plough Research Institute, Kenilworth, NJ 07033.

{ddagger} Present address: Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231.

Journal of Virology, November 2002, p. 11273-11282, Vol. 76, No. 22
0022-538X/02/$04.00+0     DOI: 10.1128/JVI.76.22.11273-11282.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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